Applying for a Japanese passport in America

Hey all, I've accepted a job offer in Japan, but the company and I are debating whether they should move forward with hiring me as a foreign national on a work visa or as a Japanese national. The problem is, I have not submitted my 国籍選択届 which I was officially supposed to do so like 6 years ago. However, I did validate that I do still have citizenship status through my koseki tohon. Would I be throwing a wrench into the process if I applied for a new Japanese passport without submitting the kokuseki sentaku todoke?

by milkt2